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##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:Maaslin2.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings Maaslin2_1.14.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.17-bioc/meat/Maaslin2.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.3 (clang-1403.0.22.14.1)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.4
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Maaslin2/DESCRIPTION’ ... OK
* this is package ‘Maaslin2’ version ‘1.14.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘Maaslin2’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
maaslin2_association_plots: no visible binding for global variable
  ‘xnames’
Undefined global functions or variables:
  xnames
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
Maaslin2 184.119  2.774 242.428
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.17-bioc/meat/Maaslin2.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL Maaslin2
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library’
* installing *source* package ‘Maaslin2’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning in checkMatrixPackageVersion() :
  Package version inconsistency detected.
TMB was built with Matrix version 1.6.0
Current Matrix version is 1.6.1.1
Please re-install 'TMB' from source using install.packages('TMB', type = 'source') or ask CRAN for a binary version of 'TMB' matching CRAN's 'Matrix' package
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Maaslin2)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> library(Maaslin2)
> 
> test_check("Maaslin2")
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2023-10-16 03:24:21.444759 INFO::Writing function arguments to log file
2023-10-16 03:24:21.579603 INFO::Verifying options selected are valid
2023-10-16 03:24:21.679104 INFO::Determining format of input files
2023-10-16 03:24:21.682281 INFO::Input format is data samples as rows and metadata samples as rows
2023-10-16 03:24:21.703121 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-10-16 03:24:21.707306 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosisnonIBD + dysbiosisUC + dysbiosisCD + antibiotics + age
2023-10-16 03:24:21.71656 INFO::Filter data based on min abundance and min prevalence
2023-10-16 03:24:21.719293 INFO::Total samples in data: 1595
2023-10-16 03:24:21.721478 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-10-16 03:24:21.738932 INFO::Total filtered features: 0
2023-10-16 03:24:21.741772 INFO::Filtered feature names from abundance and prevalence filtering:
2023-10-16 03:24:21.770499 INFO::Total filtered features with variance filtering: 0
2023-10-16 03:24:21.772935 INFO::Filtered feature names from variance filtering:
2023-10-16 03:24:21.775972 INFO::Running selected normalization method: TSS
2023-10-16 03:24:25.057022 INFO::Bypass z-score application to metadata
2023-10-16 03:24:25.059598 INFO::Running selected transform method: AST
2023-10-16 03:24:25.109689 INFO::Running selected analysis method: LM
2023-10-16 03:24:26.55633 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-10-16 03:24:27.596244 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-10-16 03:24:28.107161 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-10-16 03:24:28.514766 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-10-16 03:24:28.922687 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-10-16 03:24:29.33438 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-10-16 03:24:30.118603 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-10-16 03:24:30.497482 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-10-16 03:24:30.900507 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-10-16 03:24:31.215807 WARNING::Fitting problem for feature 9 a warning was issued
2023-10-16 03:24:31.651389 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-10-16 03:24:32.028881 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-10-16 03:24:32.429552 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-10-16 03:24:32.819321 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-10-16 03:24:33.153 WARNING::Fitting problem for feature 13 a warning was issued
2023-10-16 03:24:33.598325 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-10-16 03:24:34.012806 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-10-16 03:24:34.406283 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-10-16 03:24:34.786981 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-10-16 03:24:35.20701 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-10-16 03:24:35.60671 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-10-16 03:24:35.981886 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-10-16 03:24:36.371155 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-10-16 03:24:36.786439 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-10-16 03:24:37.169975 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-10-16 03:24:37.548687 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-10-16 03:24:37.981134 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-10-16 03:24:38.381667 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-10-16 03:24:38.770205 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-10-16 03:24:39.19675 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-10-16 03:24:39.589178 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-10-16 03:24:40.00423 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-10-16 03:24:40.404743 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-10-16 03:24:40.805452 INFO::Fitting model to feature number 32, Prevotella.copri
2023-10-16 03:24:41.188348 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-10-16 03:24:41.60006 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-10-16 03:24:41.975339 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-10-16 03:24:42.357012 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-10-16 03:24:42.764575 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-10-16 03:24:43.15763 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-10-16 03:24:43.544787 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-10-16 03:24:43.928445 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-10-16 03:24:44.329749 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-10-16 03:24:44.747852 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-10-16 03:24:45.152462 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-10-16 03:24:45.545851 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-10-16 03:24:45.914648 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-10-16 03:24:46.310267 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-10-16 03:24:46.711701 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-10-16 03:24:47.122691 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-10-16 03:24:47.514569 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-10-16 03:24:47.901316 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-10-16 03:24:48.303179 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-10-16 03:24:48.682182 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-10-16 03:24:49.085737 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-10-16 03:24:49.499842 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-10-16 03:24:49.882377 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-10-16 03:24:50.291665 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-10-16 03:24:50.684728 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-10-16 03:24:51.06926 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-10-16 03:24:51.384473 WARNING::Fitting problem for feature 58 a warning was issued
2023-10-16 03:24:51.810061 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-10-16 03:24:52.202788 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-10-16 03:24:52.55485 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-10-16 03:24:53.266271 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-10-16 03:24:53.662577 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-10-16 03:24:54.049599 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-10-16 03:24:54.420414 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-10-16 03:24:54.783476 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-10-16 03:24:55.17285 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-10-16 03:24:55.47649 WARNING::Fitting problem for feature 67 a warning was issued
2023-10-16 03:24:55.861058 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-10-16 03:24:56.238976 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-10-16 03:24:56.647363 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-10-16 03:24:57.042721 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-10-16 03:24:57.432359 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-10-16 03:24:57.828591 INFO::Fitting model to feature number 73, Dialister.invisus
2023-10-16 03:24:58.210036 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-10-16 03:24:58.584801 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-10-16 03:24:58.991949 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-10-16 03:24:59.377383 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-10-16 03:24:59.764068 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-10-16 03:25:00.50364 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-10-16 03:25:00.898833 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-10-16 03:25:01.283 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-10-16 03:25:01.70403 INFO::Fitting model to feature number 82, Escherichia.coli
2023-10-16 03:25:02.127138 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-10-16 03:25:02.517576 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-10-16 03:25:02.919248 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-10-16 03:25:03.289113 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-10-16 03:25:03.655864 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-10-16 03:25:04.222562 INFO::Counting total values for each feature
2023-10-16 03:25:04.336179 INFO::Writing filtered data to file output/features/filtered_data.tsv
2023-10-16 03:25:04.721089 INFO::Writing filtered, normalized data to file output/features/filtered_data_norm.tsv
2023-10-16 03:25:05.18337 INFO::Writing filtered, normalized, transformed data to file output/features/filtered_data_norm_transformed.tsv
2023-10-16 03:25:05.637463 INFO::Writing residuals to file output/fits/residuals.rds
2023-10-16 03:25:05.757127 INFO::Writing fitted values to file output/fits/fitted.rds
2023-10-16 03:25:05.825337 INFO::Writing extracted random effects to file output/fits/ranef.rds
2023-10-16 03:25:05.840238 INFO::Writing all results to file (ordered by increasing q-values): output/all_results.tsv
2023-10-16 03:25:05.861394 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output/significant_results.tsv
[1] "Creating output folder"
[1] "Creating output feature tables folder"
[1] "Creating output fits folder"
2023-10-16 03:25:05.908699 INFO::Writing function arguments to log file
2023-10-16 03:25:05.934595 INFO::Verifying options selected are valid
2023-10-16 03:25:05.936927 INFO::Determining format of input files
2023-10-16 03:25:05.942909 INFO::Input format is data samples as rows and metadata samples as rows
2023-10-16 03:25:05.963667 INFO::Formula for random effects: expr ~ (1 | site) + (1 | subject)
2023-10-16 03:25:05.966266 INFO::Formula for fixed effects: expr ~  diagnosis + dysbiosis + antibiotics + age
2023-10-16 03:25:05.975092 INFO::Filter data based on min abundance and min prevalence
2023-10-16 03:25:05.977511 INFO::Total samples in data: 1595
2023-10-16 03:25:05.979625 INFO::Min samples required with min abundance for a feature not to be filtered: 159.500000
2023-10-16 03:25:05.991811 INFO::Total filtered features: 0
2023-10-16 03:25:05.994331 INFO::Filtered feature names from abundance and prevalence filtering:
2023-10-16 03:25:06.019936 INFO::Total filtered features with variance filtering: 0
2023-10-16 03:25:06.022397 INFO::Filtered feature names from variance filtering:
2023-10-16 03:25:06.024812 INFO::Running selected normalization method: NONE
2023-10-16 03:25:06.029761 INFO::Bypass z-score application to metadata
2023-10-16 03:25:06.031969 INFO::Running selected transform method: AST
2023-10-16 03:25:06.080087 INFO::Running selected analysis method: LM
2023-10-16 03:25:06.083144 INFO::Fitting model to feature number 1, Bifidobacterium.adolescentis
2023-10-16 03:25:06.479497 INFO::Fitting model to feature number 2, Bifidobacterium.bifidum
2023-10-16 03:25:06.872125 INFO::Fitting model to feature number 3, Bifidobacterium.longum
2023-10-16 03:25:07.242722 INFO::Fitting model to feature number 4, Bifidobacterium.pseudocatenulatum
2023-10-16 03:25:07.621478 INFO::Fitting model to feature number 5, Collinsella.aerofaciens
2023-10-16 03:25:08.390947 INFO::Fitting model to feature number 6, Bacteroides.caccae
2023-10-16 03:25:08.764896 INFO::Fitting model to feature number 7, Bacteroides.cellulosilyticus
2023-10-16 03:25:09.115879 INFO::Fitting model to feature number 8, Bacteroides.dorei
2023-10-16 03:25:09.461867 INFO::Fitting model to feature number 9, Bacteroides.eggerthii
2023-10-16 03:25:09.848227 INFO::Fitting model to feature number 10, Bacteroides.faecis
2023-10-16 03:25:10.254205 INFO::Fitting model to feature number 11, Bacteroides.finegoldii
2023-10-16 03:25:10.631842 INFO::Fitting model to feature number 12, Bacteroides.fragilis
2023-10-16 03:25:11.002507 INFO::Fitting model to feature number 13, Bacteroides.intestinalis
2023-10-16 03:25:11.319099 WARNING::Fitting problem for feature 13 a warning was issued
2023-10-16 03:25:11.69796 INFO::Fitting model to feature number 14, Bacteroides.massiliensis
2023-10-16 03:25:12.062038 INFO::Fitting model to feature number 15, Bacteroides.ovatus
2023-10-16 03:25:12.4512 INFO::Fitting model to feature number 16, Bacteroides.salyersiae
2023-10-16 03:25:12.746965 WARNING::Fitting problem for feature 16 a warning was issued
2023-10-16 03:25:13.12626 INFO::Fitting model to feature number 17, Bacteroides.stercoris
2023-10-16 03:25:13.494604 INFO::Fitting model to feature number 18, Bacteroides.thetaiotaomicron
2023-10-16 03:25:13.872969 INFO::Fitting model to feature number 19, Bacteroides.uniformis
2023-10-16 03:25:14.251828 INFO::Fitting model to feature number 20, Bacteroides.vulgatus
2023-10-16 03:25:14.625669 INFO::Fitting model to feature number 21, Bacteroides.xylanisolvens
2023-10-16 03:25:14.999933 INFO::Fitting model to feature number 22, Bacteroidales.bacterium.ph8
2023-10-16 03:25:15.366268 INFO::Fitting model to feature number 23, Barnesiella.intestinihominis
2023-10-16 03:25:15.727788 INFO::Fitting model to feature number 24, Coprobacter.fastidiosus
2023-10-16 03:25:16.116803 INFO::Fitting model to feature number 25, Odoribacter.splanchnicus
2023-10-16 03:25:16.482596 INFO::Fitting model to feature number 26, Parabacteroides.distasonis
2023-10-16 03:25:16.858243 INFO::Fitting model to feature number 27, Parabacteroides.goldsteinii
2023-10-16 03:25:17.220275 INFO::Fitting model to feature number 28, Parabacteroides.merdae
2023-10-16 03:25:17.57645 INFO::Fitting model to feature number 29, Parabacteroides.unclassified
2023-10-16 03:25:17.953957 INFO::Fitting model to feature number 30, Paraprevotella.clara
2023-10-16 03:25:18.318195 INFO::Fitting model to feature number 31, Paraprevotella.unclassified
2023-10-16 03:25:18.668802 INFO::Fitting model to feature number 32, Prevotella.copri
2023-10-16 03:25:19.042762 INFO::Fitting model to feature number 33, Alistipes.finegoldii
2023-10-16 03:25:19.406658 INFO::Fitting model to feature number 34, Alistipes.onderdonkii
2023-10-16 03:25:19.793649 INFO::Fitting model to feature number 35, Alistipes.putredinis
2023-10-16 03:25:20.162187 INFO::Fitting model to feature number 36, Alistipes.shahii
2023-10-16 03:25:20.532619 INFO::Fitting model to feature number 37, Alistipes.unclassified
2023-10-16 03:25:20.905602 INFO::Fitting model to feature number 38, Streptococcus.salivarius
2023-10-16 03:25:21.273884 INFO::Fitting model to feature number 39, Clostridium.bolteae
2023-10-16 03:25:21.641342 INFO::Fitting model to feature number 40, Clostridium.citroniae
2023-10-16 03:25:21.999809 INFO::Fitting model to feature number 41, Clostridium.clostridioforme
2023-10-16 03:25:22.375879 INFO::Fitting model to feature number 42, Clostridium.hathewayi
2023-10-16 03:25:22.737345 INFO::Fitting model to feature number 43, Clostridium.leptum
2023-10-16 03:25:23.12576 INFO::Fitting model to feature number 44, Clostridium.nexile
2023-10-16 03:25:23.497659 INFO::Fitting model to feature number 45, Clostridium.symbiosum
2023-10-16 03:25:23.917657 INFO::Fitting model to feature number 46, Flavonifractor.plautii
2023-10-16 03:25:24.325428 INFO::Fitting model to feature number 47, Eubacterium.eligens
2023-10-16 03:25:24.667213 INFO::Fitting model to feature number 48, Eubacterium.hallii
2023-10-16 03:25:25.103129 INFO::Fitting model to feature number 49, Eubacterium.rectale
2023-10-16 03:25:25.46076 INFO::Fitting model to feature number 50, Eubacterium.siraeum
2023-10-16 03:25:25.841852 INFO::Fitting model to feature number 51, Eubacterium.sp.3.1.31
2023-10-16 03:25:26.224993 INFO::Fitting model to feature number 52, Eubacterium.ventriosum
2023-10-16 03:25:26.577157 INFO::Fitting model to feature number 53, Ruminococcus.gnavus
2023-10-16 03:25:26.951713 INFO::Fitting model to feature number 54, Ruminococcus.obeum
2023-10-16 03:25:27.315556 INFO::Fitting model to feature number 55, Ruminococcus.torques
2023-10-16 03:25:27.67113 INFO::Fitting model to feature number 56, Coprococcus.comes
2023-10-16 03:25:28.045413 INFO::Fitting model to feature number 57, Dorea.longicatena
2023-10-16 03:25:28.408609 INFO::Fitting model to feature number 58, Lachnospiraceae.bacterium.1.1.57FAA
2023-10-16 03:25:28.784814 INFO::Fitting model to feature number 59, Lachnospiraceae.bacterium.3.1.46FAA
2023-10-16 03:25:29.156102 INFO::Fitting model to feature number 60, Roseburia.hominis
2023-10-16 03:25:29.506464 INFO::Fitting model to feature number 61, Roseburia.intestinalis
2023-10-16 03:25:29.853998 INFO::Fitting model to feature number 62, Roseburia.inulinivorans
2023-10-16 03:25:30.222569 INFO::Fitting model to feature number 63, Roseburia.unclassified
2023-10-16 03:25:30.60838 INFO::Fitting model to feature number 64, Oscillibacter.unclassified
2023-10-16 03:25:30.990433 INFO::Fitting model to feature number 65, Peptostreptococcaceae.noname.unclassified
2023-10-16 03:25:31.350326 INFO::Fitting model to feature number 66, Faecalibacterium.prausnitzii
2023-10-16 03:25:31.783647 INFO::Fitting model to feature number 67, Ruminococcus.bromii
2023-10-16 03:25:32.124963 WARNING::Fitting problem for feature 67 a warning was issued
2023-10-16 03:25:32.594836 INFO::Fitting model to feature number 68, Ruminococcus.callidus
2023-10-16 03:25:32.982404 INFO::Fitting model to feature number 69, Ruminococcus.lactaris
2023-10-16 03:25:33.367538 INFO::Fitting model to feature number 70, Subdoligranulum.unclassified
2023-10-16 03:25:33.778387 INFO::Fitting model to feature number 71, Coprobacillus.unclassified
2023-10-16 03:25:34.16179 INFO::Fitting model to feature number 72, Acidaminococcus.unclassified
2023-10-16 03:25:34.310061 WARNING::Fitting problem for feature 72 a warning was issued
2023-10-16 03:25:34.743679 INFO::Fitting model to feature number 73, Dialister.invisus
2023-10-16 03:25:35.102458 INFO::Fitting model to feature number 74, Veillonella.atypica
2023-10-16 03:25:35.444671 INFO::Fitting model to feature number 75, Veillonella.dispar
2023-10-16 03:25:35.791567 INFO::Fitting model to feature number 76, Veillonella.parvula
2023-10-16 03:25:36.174925 INFO::Fitting model to feature number 77, Veillonella.unclassified
2023-10-16 03:25:36.53183 INFO::Fitting model to feature number 78, Burkholderiales.bacterium.1.1.47
2023-10-16 03:25:36.905228 INFO::Fitting model to feature number 79, Parasutterella.excrementihominis
2023-10-16 03:25:37.287671 INFO::Fitting model to feature number 80, Sutterella.wadsworthensis
2023-10-16 03:25:37.665503 INFO::Fitting model to feature number 81, Bilophila.unclassified
2023-10-16 03:25:38.070994 INFO::Fitting model to feature number 82, Escherichia.coli
2023-10-16 03:25:38.429843 INFO::Fitting model to feature number 83, Escherichia.unclassified
2023-10-16 03:25:38.782771 INFO::Fitting model to feature number 84, Klebsiella.pneumoniae
2023-10-16 03:25:39.130143 INFO::Fitting model to feature number 85, Haemophilus.parainfluenzae
2023-10-16 03:25:39.496307 INFO::Fitting model to feature number 86, Akkermansia.muciniphila
2023-10-16 03:25:39.883248 INFO::Fitting model to feature number 87, C2likevirus.unclassified
2023-10-16 03:25:40.332944 INFO::Counting total values for each feature
2023-10-16 03:25:40.409394 INFO::Writing filtered data to file output2/features/filtered_data.tsv
2023-10-16 03:25:40.766378 INFO::Writing filtered, normalized data to file output2/features/filtered_data_norm.tsv
2023-10-16 03:25:41.139092 INFO::Writing filtered, normalized, transformed data to file output2/features/filtered_data_norm_transformed.tsv
2023-10-16 03:25:41.619118 INFO::Writing residuals to file output2/fits/residuals.rds
2023-10-16 03:25:41.777666 INFO::Writing fitted values to file output2/fits/fitted.rds
2023-10-16 03:25:41.924625 INFO::Writing extracted random effects to file output2/fits/ranef.rds
2023-10-16 03:25:41.939189 INFO::Writing all results to file (ordered by increasing q-values): output2/all_results.tsv
2023-10-16 03:25:41.958627 INFO::Writing the significant results (those which are less than or equal to the threshold of 0.250000 ) to file (ordered by increasing q-values): output2/significant_results.tsv
[ FAIL 0 | WARN 8 | SKIP 0 | PASS 12 ]

[ FAIL 0 | WARN 8 | SKIP 0 | PASS 12 ]
> 
> 
> proc.time()
   user  system elapsed 
 61.732   1.196  83.792